1-203200263-A-G

Variant names:

• chr1-203200263-A-G
• rs872129

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.19 in 152,176 control chromosomes in the GnomAD database, including 3,811 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.19 (3811 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.201

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.525 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.189 AC: 28807 AN: 152058 Hom.: 3769 Cov.: 32

Gnomad AFR AF: 0.297

Gnomad AMI AF: 0.0208

Gnomad AMR AF: 0.279

Gnomad ASJ AF: 0.168

Gnomad EAS AF: 0.540

Gnomad SAS AF: 0.237

Gnomad FIN AF: 0.0542

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.0971

Gnomad OTH AF: 0.213

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.190 AC: 28908 AN: 152176 Hom.: 3811 Cov.: 32 AF XY: 0.193 AC XY: 14347 AN XY: 74378

Gnomad4 AFR AF: 0.298

Gnomad4 AMR AF: 0.280

Gnomad4 ASJ AF: 0.168

Gnomad4 EAS AF: 0.542

Gnomad4 SAS AF: 0.237

Gnomad4 FIN AF: 0.0542

Gnomad4 NFE AF: 0.0971

Gnomad4 OTH AF: 0.220

Alfa AF: 0.131 Hom.: 2562

Bravo AF: 0.214

Asia WGS AF: 0.403 AC: 1399 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.61
DANN	Benign	0.41

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs872129; hg19: chr1-203169391;